[gmx-users] Box Size in MD

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Mar 22 17:24:58 CET 2012

Hi Lara,

The cut-offs are pretty much part of the force field. One rule is that
the distance between periodic images should be larger than the cutoff.
For protein/solute simulations that translates in a minimal distance
between the solute and the wall of half the cutoff used. Another rule
is based on the solvent ordering. In water, ordering carries through
approximately four layers of water, corresponding to 1 nm. So to avoid
indirect effects through solvent ordering, it is advisable to use a
distance between periodic images of 2 nm, i.e. a distance between
solute and box wall of 1 nm.

Hope it helps,


On Thu, Mar 22, 2012 at 5:08 PM, Lara Bunte <lara.bunte at yahoo.de> wrote:
> Hello
> What size should a box have in that you do your MD? I always read that for short Lennard Jones interactions one should do a cut off with the half of the box size but what how to know a good box size?
> Thanks for help
> Greetings
> Lara
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Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands

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